comparison matchms_filtering.xml @ 5:a177ac3c752c draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e

4:357df6c47d92

<tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0">
    <description>filter and normalize mass spectrometry data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
        <requirement type="package" version="1.1.4">pandas</requirement>
    </requirements>

    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
    </environment_variables>

    <command detect_errors="exit_code"><![CDATA[
        sh ${matchms_python_cli}
    ]]> </command>

    <configfiles>
        <configfile name="matchms_python_cli">
            python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
            --spectra "$spectra" \

        <conditional name="relative_intensity">
            <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
            <when value="TRUE">
                <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." />
                <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." />
            </when>
        </conditional>

        <conditional name="mz_range">
            <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"

            </section>
            <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
        </test>
    </tests>

    <help><![CDATA[
    Documentation
        For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.

    Upstream Tools
        +-----------+---------------+--------+-----------+
        | Name      | Output File   | Format | Parameter |
        +===========+===============+========+===========+
        | RAMClustR | Mass spectra  | msp    | references|
        +-----------+---------------+--------+-----------+
        | RAMClustR | Mass spectra  | msp    | queries   |
        +-----------+---------------+--------+-----------+

    Downstream Tools
        The output is an msp file after applying the specified filters.
    ]]></help>


    <expand macro="citations"/>
</tool>

5:a177ac3c752c

<tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09">
    <description>filter and normalize mass spectrometry data</description>

    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>

    <expand macro="creator"/>

    <edam_operations>
        <edam_operation>operation_3695</edam_operation>
    </edam_operations>
    <expand macro="bio.tools"/>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        sh ${matchms_python_cli}
    ]]> </command>

    <environment_variables>
        <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
    </environment_variables>

    <configfiles>
        <configfile name="matchms_python_cli">
            python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
            --spectra "$spectra" \

        <conditional name="relative_intensity">
            <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
                   help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
            <when value="TRUE">
                <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
                <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
            </when>
        </conditional>

        <conditional name="mz_range">
            <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"

            </section>
            <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
        </test>
    </tests>

    <help>
        @HELP_matchms@
    </help>

    <expand macro="citations"/>
</tool>